Analytical methods techniques, molecular structural

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

A Brief Review of the QSAR Technique. Most of the 2D QSAR methods employ graph theoretic indices to characterize molecular structures, which have been extensively studied by Radic, Kier, and Hall [see 23]. Although these structural indices represent different aspects of the molecular structures, their physicochemical meaning is unclear. The successful applications of these topological indices combined with MLR analysis have been summarized recently. Similarly, the ADAPT system employs topological indices as well as other structural parameters (e.g., steric and quantum mechanical parameters) coupled with MLR method for QSAR analysis [24]. It has been extensively applied to QSAR/QSPR studies in analytical chemistry, toxicity analysis, and other biological activity prediction. On the other hand, parameters derived from various experiments through chemometric methods have also been used in the study of peptide QSAR, where partial least-squares (PLS) analysis has been employed [25]. 

Laser desorption methods (such as LD-ITMS) are indicated as cost-saving real-time techniques for the near future. In a single laser shot, the LDI technique coupled with Fourier-transform mass spectrometry (FTMS) can provide detailed chemical information on the polymeric molecular structure, and is a tool for direct determination of additives and contaminants in polymers. This offers new analytical capabilities to solve problems in research, development, engineering, production, technical support, competitor product analysis, and defect analysis. Laser desorption techniques are limited to surface analysis and do not allow quantitation, but exhibit superior analyte selectivity. 

The chemical world is often divided into measurers and makers of molecules. This division has deep historic roots, but it artificially impedes taking advantage of both aspects of the chemical sciences. Of key importance to all forms of chemistry are instruments and techniques that allow examination, in space and in time, of the composition and characterization of a chemical system under study. To achieve this end in a practical manner, these instruments will need to multiplex several analytical methods. They will need to meet one or more of the requirements for characterization of the products of combinatorial chemical synthesis, correlation of molecular structure with dynamic processes, high-resolution definition of three-dimensional structures and the dynamics of then-formation, and remote detection and telemetry. 

MS delivers both information about the mass and the isotope pattern of a compound and can be used for the structural analysis upon performance of MS/MS experiments. Therefore, it is a valuable tool for the identification and characterization of an analyte as well as for the identification of impurities. Potential applications are the identification of IL in fhe quality control or in environmental studies. Unwanted by-products formed during the s)mthe-sis or by the hydrolysis of components of the ILs can be identified by this method. The analysis of fhe IL itself is also a prerequisite for the analysis of compounds dissolved in fhese media, as will be ouflined in the section 14.4. Beside the identification of fhe ILs, a characterization of different properties like water miscibility and the formation of ion clusfers, providing valuable information abouf fhe molecular structure of the IL, can be performed by means of MS techniques. The majority of studies reported up to now have dealt with ILs encompassing substituted imidazolium or pyridinium cations, therefore fhe following discussion concentrates on these compounds unless otherwise stated. 

Mass spectrometry (MS) is an analytical method based on the determination of atomic or molecular masses of individual species in a sample. Information acquired allows determination of the nature, composition, and even structure of the analyte. Mass spectrometers can be classified into categories based on the mass separation technique used. Some of the instruments date back to the beginning of the twentieth century and were used for the study of charged particles or ionised atoms using magnetic fields, while others of modest performance, such as bench-top models often used in conjunction with chromatography, rely on different principles for mass analysis. Continuous improvements to the instruments, miniaturisation and advances in new ionisation techniques have made MS one of the methods with the widest application range because of its flexibility and extreme sensitivity. 

FTMS also has the potential of becoming an important tool for determining molecular structure. Traditionally, mass spectrometry has been rather limited in its ability to determine the structure of an unknown compound unambiguously. Additional structural methods, such as nuclear magnetic resonance or crystallography, are commonly used in conjunction with mass spectrometry to elucidate the identity of a molecule. However, when the amount of sample is severely limited or when the sample is a component in a complex mixture, mass spectrometry is often one of the few analytical techniques that can be used. 

In the case of an unknown chemical, or where resonance overlap occurs, it may be necessary to call upon the full arsenal of NMR methods. To confirm a heteronuclear coupling, the normal H NMR spectrum is compared with 1H 19F and/or XH 31 P NMR spectra. After this, and, in particular, where a strong background is present, the various 2-D NMR spectra are recorded. Homonuclear chemical shift correlation experiments such as COSY and TOCSY (or some of their variants) provide information on coupled protons, even networks of protons (1), while the inverse detected heteronuclear correlation experiments such as HMQC and HMQC/TOCSY provide similar information but only for protons coupling to heteronuclei, for example, the pairs 1H-31P and - C. Although interpretation of these data provides abundant information on the molecular structure, the results obtained with other analytical or spectrometric techniques must be taken into account as well. The various methods of MS and gas chromatography/Fourier transform infrared (GC/FTIR) spectroscopy supply complementary information to fully resolve or confirm the structure. Unambiguous identification of an unknown chemical requires consistent results from all spectrometric techniques employed. 

Characterization Techniques for Pitch Materials. Among a number of characterization techniques developed in Japan, the technique due to the members of the Society of Heavy Oil, led by Kunugi, stands out as particularly useful. The analytical data are treated by computer methods to construct average molecular structures for the carbonaceous materials. Sanada s group in Hokkaido University used high-temperature NMR and ESR data obtained by in situ measurements of pitch materials in molten salt (21). Much information on mesophase behavior during the heat-treatment process was obtained in this way. 

In this review results from two surface science methods are presented. Electron Spectroscopy for Chemical Analysis (ESCA or XPS) is a widely used method for the study of organic and polymeric surfaces, metal corrosion and passivation studies and metallization of polymers (la). However, one major accent of our work has been the development of complementary ion beam methods for polymer surface analysis. Of the techniques deriving from ion beam interactions, Secondary Ion Mass Spectrometry (SIMS), used as a surface analytical method, has many advantages over electron spectroscopies. Such benefits include superior elemental sensitivity with a ppm to ppb detection limit, the ability to detect molecular secondary ions which are directly related to the molecular structure, surface compositional sensitivity due in part to the matrix sensitivity of secondary emission, and mass spectrometric isotopic sensitivity. The major difficulties which limit routine analysis with SIMS include sample damage due to sputtering, a poor understanding of the relationship between matrix dependent secondary emission and molecular surface composition, and difficulty in obtaining reproducible, accurate quantitative molecular information. Thus, we have worked to overcome the limitations for quantitation, and the present work will report the results of these studies. 

By convention, the term branched implies that the polymer molecules are discrete, which is to say that their sizes can be measured by at least some of the usual analytical methods described in Chapter 3. A network polymer is an interconnected branch polymer. The molecular weight of such polymers is infinite, in the sense that it is too high to be measured by standard techniques. If the average functionality of a mixture of monomers is greater than 2, reaction to sufficiently high conversion yields network structures (p. 174). 

---